Complete surgical resection is the treatment of choice for primary gastrointestinal stromal tumor (GIST), even with current advances in molecular targeting therapy with imatinib and sunitinib. In recent years, function-preserving and minimally invasive surgeries have also been performed as treatment strategies for submucosal tumors, including GISTs that are clinically diagnosed as low-risk. It is crucial, however, not to compromise radicality when indicating these procedures. On the other hand, a multidisciplinary treatment, including surgical resection, is necessary even for the treatment of advanced or metastatic/ recurrent GISTs in which the treatment of choice is imatinib therapy. Furthermore, surgical treatment is expected to be effective for resectable liver metastases, secondary resistance to imatinib, or residual tumors responding to imatinib. In this regard, surgical resection as a multidisciplinary treatment is considered to have gained recognition as an important option. However, sufficient evidence is lacking, and thus, the results of ongoing clinical trials are highly anticipated. For the surgical treatment of GIST, it is important to select patients carefully based on objective data to obtain maximum therapeutic effects.